For the control problem of micro-flow controller using piezoelectric ceramics as driving components in the electric propulsion system, we directly utilize the collected rate of flow as the state and give a closed-loop control method which can eliminate the hysteresis and creep characteristics of piezoelectric ceramic. Through the experiment with the real flow control system, it is verified that the control method can effectively stabilize and follow the rate of flow, and the influence of ambient temperature on the closed-loop flow control is analysed. Then by analysing the power spectral density analysis of the obtained flow data, the flow noise is significant in the low frequency band for different closed-loop target flows, while in order to reduce the flow noise, the flow sampling frequency should be increased.